February 2019 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Checkpoint-restart with DMPlex objects
by Lisandro Dalcin 28 Feb '19

28 Feb '19

On Fri, 20 Jul 2018 at 12:34, Lawrence Mitchell <wence(a)gmx.li> wrote: > Dear petsc-dev, > > I'm once again revisiting doing "proper" checkpoint-restart cycles. I > would like to leverage the existing PETSc stuff for this as much as > possible, but I am a bit lost as to what is implemented, and what is > missing. > > I have: > > - A (distributed) DMPlex defining the topology > > Not sure if it will be really useful, but I have some code I can share with you to save/load DMPlex objects using PETSc's native binary viewers (either stdio or MPI-IO). A minor (or big?) issue is that loads are sequential, you have to distribute/overlap afterwards, but this is the way it works with most mesh readers. I should be really putting that code in PETSc, but... 1) It is most likely not 100% general, I'm not supporting the new DMField for coordinates. 2) Herr Prof. Matt seems to be in favor of all these fancy HDF5-based formats (https://xkcd.com/927/) -- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Extreme Computing Research Center (ECRC) King Abdullah University of Science and Technology (KAUST) http://ecrc.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 0109 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459

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Re: [petsc-dev] [petsc-users] (no subject)
by Stefano Zampini 27 Feb '19

27 Feb '19

This is how I fixed this. You should configure PETSc using these libraries from brew. '--with-giflib-dir=/usr/local', '--with-libjpeg-dir=/usr/local', '--with-libpng-dir=/usr/local', '--with-opengl-dir=/usr/X11', '--with-zlib-dir=/usr/local/opt/zlib', > On Feb 27, 2019, at 4:01 PM, DAFNAKIS PANAGIOTIS via petsc-users <petsc-users(a)mcs.anl.gov> wrote: > > Hi everybody, > > I am trying to install PETSc version 3.10.3 on OSX Sierra 10.13.6 with the following configure options > ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --PETSC_ARCH=sierra-dbg --with-debugging=1 --download-hypre=1 --with-x=0 > > however I am getting the following error messages when I do 'make check'. See below the resulting message. Any suggestions? > > Thanks, > > --Panos > > panos@Sierra-iMac:~/Softwares/PETSc-Bitbucket/PETSc$ make PETSC_DIR=/Users/panos/Softwares/PETSc-Bitbucket/PETSc PETSC_ARCH=sierra-dbg check > Running test examples to verify correct installation > Using PETSC_DIR=/Users/panos/Softwares/PETSc-Bitbucket/PETSc and PETSC_ARCH=sierra-dbg > make[2]: [ex19.PETSc] Error 2 (ignored) > *******************Error detected during compile or link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials ex19 > ********************************************************************************* > mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3 -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/include -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/include `pwd`/ex19.c > mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3 -o ex19 ex19.o -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.3/lib -L/usr/local/Cellar/mpich/3.3/lib -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -Wl,-rpath,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -Wl,-rpath,/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -L/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -Wl,-rpath,/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -L/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -lpetsc -lHYPRE -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lGFXShared -lGLU -lGL -lGLImage -lCVMSPluginSupport -lFontParser -lFontRegistry -lJPEG -lTIFF -lPng -lGIF -lJP2 -lRadiance -lCoreVMClient -ldl > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit.tbd and library file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator.tbd and library file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices.tbd and library file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics.tbd and library file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//Security.framework/Versions/A/Security.tbd and library file /System/Library/Frameworks//Security.framework/Versions/A/Security are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices.tbd and library file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation.tbd and library file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL.tbd and library file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface.tbd and library file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText.tbd and library file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO.tbd and library file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork.tbd and library file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration.tbd and library file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL.tbd and library file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio.tbd and library file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox.tbd and library file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd and library file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement.tbd and library file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and library file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of sync. Falling back to library file for linking. > Undefined symbols for architecture x86_64: > "_jpeg_CreateCompress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_destroy_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_finish_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_set_defaults", referenced from: > import-atom in libpetsc.dylib > "_jpeg_start_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_std_error", referenced from: > import-atom in libpetsc.dylib > "_jpeg_stdio_dest", referenced from: > import-atom in libpetsc.dylib > "_jpeg_write_scanlines", referenced from: > import-atom in libpetsc.dylib > "_png_create_info_struct", referenced from: > import-atom in libpetsc.dylib > "_png_create_write_struct", referenced from: > import-atom in libpetsc.dylib > "_png_destroy_write_struct", referenced from: > import-atom in libpetsc.dylib > "_png_init_io", referenced from: > import-atom in libpetsc.dylib > "_png_set_IHDR", referenced from: > import-atom in libpetsc.dylib > "_png_set_PLTE", referenced from: > import-atom in libpetsc.dylib > "_png_set_longjmp_fn", referenced from: > import-atom in libpetsc.dylib > "_png_write_end", referenced from: > import-atom in libpetsc.dylib > "_png_write_info", referenced from: > import-atom in libpetsc.dylib > "_png_write_row", referenced from: > import-atom in libpetsc.dylib > ld: symbol(s) not found for architecture x86_64 > clang: error: linker command failed with exit code 1 (use -v to see invocation) > make[3]: [ex19] Error 1 (ignored) > /usr/bin/dsymutil ex19 > error: cannot parse the debug map for 'ex19': No such file or directory > make[3]: *** [ex19] Error 1 > rm ex19.o > 1,5c1,2 > < lid velocity = 0.0016, prandtl # = 1., grashof # = 1. > < 0 SNES Function norm 0.0406612 > < 1 SNES Function norm 4.12227e-06 > < 2 SNES Function norm 6.098e-11 > < Number of SNES iterations = 2 > --- >> [proxy:0:[email protected]] HYDU_create_process (utils/launch/launch.c:74): execvp error on file ./ex19 (No such file or directory) >> [proxy:0:[email protected]] HYDU_create_process (utils/launch/launch.c:74): execvp error on file ./ex19 (No such file or directory) > /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials > Possible problem with ex19_hypre, diffs above > ========================================= > *******************Error detected during compile or link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials ex5f > ********************************************************* > mpif90 -c -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/include -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/include -o ex5f.o ex5f.F90 > mpif90 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -o ex5f ex5f.o -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.3/lib -L/usr/local/Cellar/mpich/3.3/lib -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -Wl,-rpath,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -Wl,-rpath,/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -L/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -Wl,-rpath,/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -L/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -lpetsc -lHYPRE -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lGFXShared -lGLU -lGL -lGLImage -lCVMSPluginSupport -lFontParser -lFontRegistry -lJPEG -lTIFF -lPng -lGIF -lJP2 -lRadiance -lCoreVMClient -ldl > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit.tbd and library file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator.tbd and library file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices.tbd and library file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics.tbd and library file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//Security.framework/Versions/A/Security.tbd and library file /System/Library/Frameworks//Security.framework/Versions/A/Security are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices.tbd and library file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation.tbd and library file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL.tbd and library file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface.tbd and library file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText.tbd and library file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO.tbd and library file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork.tbd and library file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration.tbd and library file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL.tbd and library file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio.tbd and library file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox.tbd and library file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd and library file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement.tbd and library file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement are out of sync. Falling back to library file for linking. > ld: warning: text-based stub file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and library file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of sync. Falling back to library file for linking. > Undefined symbols for architecture x86_64: > "_jpeg_CreateCompress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_destroy_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_finish_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_set_defaults", referenced from: > import-atom in libpetsc.dylib > "_jpeg_start_compress", referenced from: > import-atom in libpetsc.dylib > "_jpeg_std_error", referenced from: > import-atom in libpetsc.dylib > "_jpeg_stdio_dest", referenced from: > import-atom in libpetsc.dylib > "_jpeg_write_scanlines", referenced from: > import-atom in libpetsc.dylib > "_png_create_info_struct", referenced from: > import-atom in libpetsc.dylib > "_png_create_write_struct", referenced from: > import-atom in libpetsc.dylib > "_png_destroy_write_struct", referenced from: > import-atom in libpetsc.dylib > "_png_init_io", referenced from: > import-atom in libpetsc.dylib > "_png_set_IHDR", referenced from: > import-atom in libpetsc.dylib > "_png_set_PLTE", referenced from: > import-atom in libpetsc.dylib > "_png_set_longjmp_fn", referenced from: > import-atom in libpetsc.dylib > "_png_write_end", referenced from: > import-atom in libpetsc.dylib > "_png_write_info", referenced from: > import-atom in libpetsc.dylib > "_png_write_row", referenced from: > import-atom in libpetsc.dylib > ld: symbol(s) not found for architecture x86_64 > collect2: error: ld returned 1 exit status > make[3]: [ex5f] Error 1 (ignored) > rm ex5f.o > Completed test examples

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by DAFNAKIS PANAGIOTIS 27 Feb '19

27 Feb '19

Hi everybody, I am trying to install PETSc version 3.10.3 on OSX Sierra 10.13.6 with the following configure options ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --PETSC_ARCH=sierra-dbg --with-debugging=1 --download-hypre=1 --with-x=0 however I am getting the following error messages when I do 'make check'. See below the resulting message. Any suggestions? Thanks, --Panos panos@Sierra-iMac:~/Softwares/PETSc-Bitbucket/PETSc$ make PETSC_DIR=/Users/panos/Softwares/PETSc-Bitbucket/PETSc PETSC_ARCH=sierra-dbg check Running test examples to verify correct installation Using PETSC_DIR=/Users/panos/Softwares/PETSc-Bitbucket/PETSc and PETSC_ARCH=sierra-dbg make[2]: [ex19.PETSc] Error 2 (ignored) *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials ex19 ********************************************************************************* mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3 -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/include -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/include `pwd`/ex19.c mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3 -o ex19 ex19.o -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.3/lib -L/usr/local/Cellar/mpich/3.3/lib -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -Wl,-rpath,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -Wl,-rpath,/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -L/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -Wl,-rpath,/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -L/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -lpetsc -lHYPRE -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lGFXShared -lGLU -lGL -lGLImage -lCVMSPluginSupport -lFontParser -lFontRegistry -lJPEG -lTIFF -lPng -lGIF -lJP2 -lRadiance -lCoreVMClient -ldl ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit.tbd and library file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator.tbd and library file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices.tbd and library file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics.tbd and library file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//Security.framework/Versions/A/Security.tbd and library file /System/Library/Frameworks//Security.framework/Versions/A/Security are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices.tbd and library file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation.tbd and library file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL.tbd and library file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface.tbd and library file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText.tbd and library file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO.tbd and library file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork.tbd and library file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration.tbd and library file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL.tbd and library file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio.tbd and library file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox.tbd and library file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd and library file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement.tbd and library file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and library file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of sync. Falling back to library file for linking. Undefined symbols for architecture x86_64: "_jpeg_CreateCompress", referenced from: import-atom in libpetsc.dylib "_jpeg_destroy_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_finish_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_set_defaults", referenced from: import-atom in libpetsc.dylib "_jpeg_start_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_std_error", referenced from: import-atom in libpetsc.dylib "_jpeg_stdio_dest", referenced from: import-atom in libpetsc.dylib "_jpeg_write_scanlines", referenced from: import-atom in libpetsc.dylib "_png_create_info_struct", referenced from: import-atom in libpetsc.dylib "_png_create_write_struct", referenced from: import-atom in libpetsc.dylib "_png_destroy_write_struct", referenced from: import-atom in libpetsc.dylib "_png_init_io", referenced from: import-atom in libpetsc.dylib "_png_set_IHDR", referenced from: import-atom in libpetsc.dylib "_png_set_PLTE", referenced from: import-atom in libpetsc.dylib "_png_set_longjmp_fn", referenced from: import-atom in libpetsc.dylib "_png_write_end", referenced from: import-atom in libpetsc.dylib "_png_write_info", referenced from: import-atom in libpetsc.dylib "_png_write_row", referenced from: import-atom in libpetsc.dylib ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: [ex19] Error 1 (ignored) /usr/bin/dsymutil ex19 error: cannot parse the debug map for 'ex19': No such file or directory make[3]: *** [ex19] Error 1 rm ex19.o 1,5c1,2 < lid velocity = 0.0016, prandtl # = 1., grashof # = 1. < 0 SNES Function norm 0.0406612 < 1 SNES Function norm 4.12227e-06 < 2 SNES Function norm 6.098e-11 < Number of SNES iterations = 2 --- > [proxy:0:[email protected]] HYDU_create_process (utils/launch/launch.c:74): execvp error on file ./ex19 (No such file or directory) > [proxy:0:[email protected]] HYDU_create_process (utils/launch/launch.c:74): execvp error on file ./ex19 (No such file or directory) /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials Possible problem with ex19_hypre, diffs above ========================================= *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /Users/panos/Softwares/PETSc-Bitbucket/PETSc/src/snes/examples/tutorials ex5f ********************************************************* mpif90 -c -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/include -I/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/include -o ex5f.o ex5f.F90 mpif90 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -o ex5f ex5f.o -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -L/Users/panos/Softwares/PETSc-Bitbucket/PETSc/sierra-dbg/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.3/lib -L/usr/local/Cellar/mpich/3.3/lib -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.3.0 -Wl,-rpath,/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -Wl,-rpath,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -Wl,-rpath,/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -L/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources -Wl,-rpath,/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -L/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources -lpetsc -lHYPRE -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lGFXShared -lGLU -lGL -lGLImage -lCVMSPluginSupport -lFontParser -lFontRegistry -lJPEG -lTIFF -lPng -lGIF -lJP2 -lRadiance -lCoreVMClient -ldl ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.tbd and library file /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/Versions/A/CoreFoundation are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit.tbd and library file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator.tbd and library file /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices.tbd and library file /System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics.tbd and library file /System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//Security.framework/Versions/A/Security.tbd and library file /System/Library/Frameworks//Security.framework/Versions/A/Security are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices.tbd and library file /System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation.tbd and library file /System/Library/Frameworks//Foundation.framework/Versions/C/Foundation are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL.tbd and library file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface.tbd and library file /System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText.tbd and library file /System/Library/Frameworks//CoreText.framework/Versions/A/CoreText are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO.tbd and library file /System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis.tbd and library file /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork.tbd and library file /System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList.tbd and library file /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration.tbd and library file /System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL.tbd and library file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio.tbd and library file /System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox.tbd and library file /System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd and library file /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement.tbd and library file /System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and library file /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of sync. Falling back to library file for linking. Undefined symbols for architecture x86_64: "_jpeg_CreateCompress", referenced from: import-atom in libpetsc.dylib "_jpeg_destroy_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_finish_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_set_defaults", referenced from: import-atom in libpetsc.dylib "_jpeg_start_compress", referenced from: import-atom in libpetsc.dylib "_jpeg_std_error", referenced from: import-atom in libpetsc.dylib "_jpeg_stdio_dest", referenced from: import-atom in libpetsc.dylib "_jpeg_write_scanlines", referenced from: import-atom in libpetsc.dylib "_png_create_info_struct", referenced from: import-atom in libpetsc.dylib "_png_create_write_struct", referenced from: import-atom in libpetsc.dylib "_png_destroy_write_struct", referenced from: import-atom in libpetsc.dylib "_png_init_io", referenced from: import-atom in libpetsc.dylib "_png_set_IHDR", referenced from: import-atom in libpetsc.dylib "_png_set_PLTE", referenced from: import-atom in libpetsc.dylib "_png_set_longjmp_fn", referenced from: import-atom in libpetsc.dylib "_png_write_end", referenced from: import-atom in libpetsc.dylib "_png_write_info", referenced from: import-atom in libpetsc.dylib "_png_write_row", referenced from: import-atom in libpetsc.dylib ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make[3]: [ex5f] Error 1 (ignored) rm ex5f.o Completed test examples

1 0

Re: [petsc-dev] Checkpoint-restart with DMPlex objects
by Hapla Vaclav 27 Feb '19

27 Feb '19

> On 20 Dec 2018, at 01:06, Jed Brown <jed(a)jedbrown.org> wrote: > > Hapla Vaclav via petsc-dev <petsc-dev(a)mcs.anl.gov> writes: > >> So my overall idea (which I presented also at this year's User Meeting >> in London and nobody has objected yet), is that some FE codes could >> potentially use only this for both checkpointing and >> viewing. Advantages would include removing the redundancy in storage >> (reducing the file size) and increased interoperability with 3rd party >> tools. > > This is great in principle, but note that visualization files often > contain diagnostic quantities like pressure, temperature, and vorticity > while checkpoint files contain only state variables like density, > momentum, and total energy. Although one can be derived from the other, > it requires an equation of state (an arbitrarily complex constitutive > model) and/or compatible derivatives, both of which are so cumbersome to > provide to offline visualization that almost nobody has an appetite for > it. I somehow forgot to reply. I meant mainly the topological and geometrical information. What fields are dumped in which stage is for me the matter of the concrete FE code. HDF5 allows to add different data at different stages to the same file. If there is something extra just for visualization purposes, it doesn't prevent one to use the same file to start the simulation over or load a checkpoint. For me it's mainly important that all reads/writes can be done in parallel and the topo/geo information is reused all the time. > > It certainly makes sense to use the same format that can include > arbitrary diagnostic quantities. I think that should be provided by an > extensible Viewer filter so the caller (e.g., a TS monitor) can just > call VecView and the viewer's configuration determines which diagnostic > and/or state quantities to include. Sounds good but such functionality is out of my scope for foreseeable future. > > Note that Vec holds a reference to its DM so it can determine whether > the topology is already present in the output file and link itself > appropriately. There should be no assumption that there is only one DM > or that it has already been written. Thanks Vaclav

1 0

KSPMonitor and petsc4py
by Pierre Jolivet 25 Feb '19

25 Feb '19

I’m not sure this is the expected behavior. Is it? $ git diff ex100.py diff --git a/src/ksp/ksp/examples/tutorials/ex100.py b/src/ksp/ksp/examples/tutorials/ex100.py index dbb3f8e012..051637ce1d 100644 --- a/src/ksp/ksp/examples/tutorials/ex100.py +++ b/src/ksp/ksp/examples/tutorials/ex100.py @@ -29,6 +29,7 @@ def RunTest(): ksp.setOperators(A, A) ksp.setFromOptions() ksp.solve(b, x) + ksp.solve(b, x) r = b.duplicate() A.mult(x, r) $ mpirun -np 8 python ./ex100.py -ksp_converged_reason -ksp_monitor 0 KSP Residual norm 5.101520253035e-04 1 KSP Residual norm 1.168905135944e-03 [..] 12 KSP Residual norm 5.101520253035e-05 13 KSP Residual norm 7.504522604366e-20 Linear solve converged due to CONVERGED_RTOL iterations 13 13 KSP Residual norm 5.101520253035e-04 14 KSP Residual norm 1.168905135944e-03 [..] 25 KSP Residual norm 5.101520253035e-05 26 KSP Residual norm 7.504522604366e-20 Linear solve converged due to CONVERGED_RTOL iterations 26 Shouldn’t the iterate number be reset to 0 for the 2nd KSPSolve? Thanks, Pierre

1 0

Re: [petsc-dev] Errors in MatSetValuesBlockedLocal() when using AIJ, but not BAIJ!
by Smith, Barry F. 21 Feb '19

21 Feb '19

> On Feb 21, 2019, at 8:28 PM, Mills, Richard Tran <rtmills(a)anl.gov> wrote: > > On 2/21/19 1:48 PM, Smith, Barry F. wrote: >> >>> On Feb 20, 2019, at 12:50 PM, Mills, Richard Tran via petsc-dev <petsc-dev(a)mcs.anl.gov> >>> wrote: >>> >>> Folks, >>> >>> I'm working with some PFLOTRAN examples, and I've been scratching my head for a while at errors that are being generated in MatSetValuesBlockedLocal(), related to new nonzeros requiring a malloc. E.g., >>> >>> [0]PETSC ERROR: Argument out of range >>> [0]PETSC ERROR: New nonzero at (2,0) caused a malloc >>> >>> The strange thing is that all of these examples run fine when I use the PFLOTRAN default BAIJ matrix type (with blocks column-oriented) -- I only see the issue when I switch to using AIJ. If I set the matrix option MAT_NEW_NONZERO_ALLOCATION_ERR to PETSC_FALSE to allow things to run with AIJ, everything seems to work perfectly. (And once the Jacobian matrix is constructed the first time, the memory usage is not growing according to what I see from -malloc_log.) >>> >>> I've spent some time poking around with a debugger in the variants of MatSetValues() and MatXAIJSetPreallocation(), and I haven't been able make much progress in determining why I'm seeing this in AIJ vs. BAIJ -- it's easy to get confused looking at this code, and it's going to take me more time to follow what is going on than I've had to spare so far. So, I've got a few questions. First, should it even be possible to see what I am seeing? That is, if the MatSetValuesBlocked() routine is not causing new allocations when using BAIJ, should this be possible with AIJ? >>> >> >> Sure, because the preallocation for BAIJ matrix is by block, while for AIJ it is by point (even if you provide a block size to AIJ). So long as the new entry is within an allocated block it will not trigger an error with BAIJ but may with AIJ. >> > Hmm. It seems that I've misunderstood what MatXAIJSetPreallocation() is supposed to do. I thought that if I pass in a blocksize > 1, MatXAIJSetPreallocation() will turn the block-row preallocation into the equivalent scalar-row stuff. This seems to be what is happening in the code, unless I'm reading this wrong: > > [...] > 304: } else { /* Convert block-row precallocation to scalar-row */ > 305: PetscInt i,m,*sdnnz,*sonnz; > 306: MatGetLocalSize(A,&m,NULL); > 307: PetscMalloc2((!!dnnz)*m,&sdnnz,(!!onnz)*m,&sonnz); > 308: for (i=0; i<m; i++) { > 309: if (dnnz) sdnnz[i] = dnnz[i/bs] * bs; > 310: if (onnz) sonnz[i] = onnz[i/bs] * bs; > 311: } > 312: MatSeqAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL); > 313: MatMPIAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL,0,onnz ? sonnz : NULL); > [...] I think your understanding above is correct. > > Though might something be happening later that reduces the amount of nonzeros allocated, since the "dense" blocks of the matrix actually will have zero entries that never get a value set? > > Something does appear to be screwy when I look at the "-snes_view" output for a time-dependent problem where I see these errors. When using BAIJ, at every time step I see > > Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes > type: seqbaij > rows=144, cols=144, bs=3 > total: nonzeros=2304, allocated nonzeros=2304 > total number of mallocs used during MatSetValues calls =0 > block size is 3 > > but when I switch to AIJ, I initially see > > Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes > type: seqaij > rows=144, cols=144, bs=3 > total: nonzeros=1584, allocated nonzeros=3324 > total number of mallocs used during MatSetValues calls =68 > using I-node routines: found 96 nodes, limit used is 5 > > but as things progress, the allocated nonzeros and mallocs count keeps growing; by step 43 I'm seeing > > total: nonzeros=1584, allocated nonzeros=115524 > total number of mallocs used during MatSetValues calls =7548 > > If I dump the matrices and look at them in something like Octave, the matrices from the BAIJ and AIJ runs appear identical within round-off error, and we certainly aren't adding any entries at each step. Why should PETSc keep calling malloc() at each MatSetValues() call, then? I suspect a bug somewhere in the AIJ case call sequence of MatSetValuesBlockedLocal() --> MatSetValuesBlocked() --> MatSetValues() --> MatSetValues_SeqAIJ(). I have trouble following all of the logic in matsetvaluesseqaij_(), though, so I guess I'm going to have try harder to understand why MatSeqXAIJReallocateAIJ() is being hit there. > > Any educated guesses about what might be going wrong would be appreciated. There is a lot of PETSc code I'm not familiar with involved here. Suggest a breakpoint in the MatSetValues_SeqAIJ location where the malloc() is done to determine why the mallocs keep getting called. Barry > > Cheers, > Richard > > >> >> Barry >> >> >>> (Clearly it *is* possible, but should it be?) I'm still trying to figure out if there is something wrong with what PFLOTRAN is doing, vs. something going wrong somewhere inside PETSc. >>> >>> Any hints about what to look at from someone with more familiarity with this code would be appreciated. >>> >>> --Richard >>> >

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Re: [petsc-dev] Errors in MatSetValuesBlockedLocal() when using AIJ, but not BAIJ!
by Jed Brown 21 Feb '19

21 Feb '19

What's your minimal reproducer? "Mills, Richard Tran via petsc-dev" <petsc-dev(a)mcs.anl.gov> writes: > On 2/21/19 1:48 PM, Smith, Barry F. wrote: > > > > > > On Feb 20, 2019, at 12:50 PM, Mills, Richard Tran via petsc-dev <petsc-dev(a)mcs.anl.gov><mailto:[email protected]> wrote: > > Folks, > > I'm working with some PFLOTRAN examples, and I've been scratching my head for a while at errors that are being generated in MatSetValuesBlockedLocal(), related to new nonzeros requiring a malloc. E.g., > > [0]PETSC ERROR: Argument out of range > [0]PETSC ERROR: New nonzero at (2,0) caused a malloc > > The strange thing is that all of these examples run fine when I use the PFLOTRAN default BAIJ matrix type (with blocks column-oriented) -- I only see the issue when I switch to using AIJ. If I set the matrix option MAT_NEW_NONZERO_ALLOCATION_ERR to PETSC_FALSE to allow things to run with AIJ, everything seems to work perfectly. (And once the Jacobian matrix is constructed the first time, the memory usage is not growing according to what I see from -malloc_log.) > > I've spent some time poking around with a debugger in the variants of MatSetValues() and MatXAIJSetPreallocation(), and I haven't been able make much progress in determining why I'm seeing this in AIJ vs. BAIJ -- it's easy to get confused looking at this code, and it's going to take me more time to follow what is going on than I've had to spare so far. So, I've got a few questions. First, should it even be possible to see what I am seeing? That is, if the MatSetValuesBlocked() routine is not causing new allocations when using BAIJ, should this be possible with AIJ? > > > > > Sure, because the preallocation for BAIJ matrix is by block, while for AIJ it is by point (even if you provide a block size to AIJ). So long as the new entry is within an allocated block it will not trigger an error with BAIJ but may with AIJ. > > Hmm. It seems that I've misunderstood what MatXAIJSetPreallocation() is supposed to do. I thought that if I pass in a blocksize > 1, MatXAIJSetPreallocation() will turn the block-row preallocation into the equivalent scalar-row stuff. This seems to be what is happening in the code, unless I'm reading this wrong: > > [...] > 304: } else { /* Convert block-row precallocation to scalar-row */ > 305: PetscInt i,m,*sdnnz,*sonnz; > 306: MatGetLocalSize(A,&m,NULL); > 307: PetscMalloc2((!!dnnz)*m,&sdnnz,(!!onnz)*m,&sonnz); > 308: for (i=0; i<m; i++) { > 309: if (dnnz) sdnnz[i] = dnnz[i/bs] * bs; > 310: if (onnz) sonnz[i] = onnz[i/bs] * bs; > 311: } > 312: MatSeqAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL); > 313: MatMPIAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL,0,onnz ? sonnz : NULL); > [...] > > Though might something be happening later that reduces the amount of nonzeros allocated, since the "dense" blocks of the matrix actually will have zero entries that never get a value set? > > Something does appear to be screwy when I look at the "-snes_view" output for a time-dependent problem where I see these errors. When using BAIJ, at every time step I see > > Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes > type: seqbaij > rows=144, cols=144, bs=3 > total: nonzeros=2304, allocated nonzeros=2304 > total number of mallocs used during MatSetValues calls =0 > block size is 3 > > but when I switch to AIJ, I initially see > > Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes > type: seqaij > rows=144, cols=144, bs=3 > total: nonzeros=1584, allocated nonzeros=3324 > total number of mallocs used during MatSetValues calls =68 > using I-node routines: found 96 nodes, limit used is 5 > > but as things progress, the allocated nonzeros and mallocs count keeps growing; by step 43 I'm seeing > > total: nonzeros=1584, allocated nonzeros=115524 > total number of mallocs used during MatSetValues calls =7548 > > If I dump the matrices and look at them in something like Octave, the matrices from the BAIJ and AIJ runs appear identical within round-off error, and we certainly aren't adding any entries at each step. Why should PETSc keep calling malloc() at each MatSetValues() call, then? I suspect a bug somewhere in the AIJ case call sequence of MatSetValuesBlockedLocal() --> MatSetValuesBlocked() --> MatSetValues() --> MatSetValues_SeqAIJ(). I have trouble following all of the logic in matsetvaluesseqaij_(), though, so I guess I'm going to have try harder to understand why MatSeqXAIJReallocateAIJ() is being hit there. > > Any educated guesses about what might be going wrong would be appreciated. There is a lot of PETSc code I'm not familiar with involved here. > > Cheers, > Richard > > > > > > Barry > > > > (Clearly it *is* possible, but should it be?) I'm still trying to figure out if there is something wrong with what PFLOTRAN is doing, vs. something going wrong somewhere inside PETSc. > > Any hints about what to look at from someone with more familiarity with this code would be appreciated. > > --Richard

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Re: [petsc-dev] Errors in MatSetValuesBlockedLocal() when using AIJ, but not BAIJ!
by Mills, Richard Tran 21 Feb '19

21 Feb '19

On 2/21/19 1:48 PM, Smith, Barry F. wrote: On Feb 20, 2019, at 12:50 PM, Mills, Richard Tran via petsc-dev <petsc-dev(a)mcs.anl.gov><mailto:[email protected]> wrote: Folks, I'm working with some PFLOTRAN examples, and I've been scratching my head for a while at errors that are being generated in MatSetValuesBlockedLocal(), related to new nonzeros requiring a malloc. E.g., [0]PETSC ERROR: Argument out of range [0]PETSC ERROR: New nonzero at (2,0) caused a malloc The strange thing is that all of these examples run fine when I use the PFLOTRAN default BAIJ matrix type (with blocks column-oriented) -- I only see the issue when I switch to using AIJ. If I set the matrix option MAT_NEW_NONZERO_ALLOCATION_ERR to PETSC_FALSE to allow things to run with AIJ, everything seems to work perfectly. (And once the Jacobian matrix is constructed the first time, the memory usage is not growing according to what I see from -malloc_log.) I've spent some time poking around with a debugger in the variants of MatSetValues() and MatXAIJSetPreallocation(), and I haven't been able make much progress in determining why I'm seeing this in AIJ vs. BAIJ -- it's easy to get confused looking at this code, and it's going to take me more time to follow what is going on than I've had to spare so far. So, I've got a few questions. First, should it even be possible to see what I am seeing? That is, if the MatSetValuesBlocked() routine is not causing new allocations when using BAIJ, should this be possible with AIJ? Sure, because the preallocation for BAIJ matrix is by block, while for AIJ it is by point (even if you provide a block size to AIJ). So long as the new entry is within an allocated block it will not trigger an error with BAIJ but may with AIJ. Hmm. It seems that I've misunderstood what MatXAIJSetPreallocation() is supposed to do. I thought that if I pass in a blocksize > 1, MatXAIJSetPreallocation() will turn the block-row preallocation into the equivalent scalar-row stuff. This seems to be what is happening in the code, unless I'm reading this wrong: [...] 304: } else { /* Convert block-row precallocation to scalar-row */ 305: PetscInt i,m,*sdnnz,*sonnz; 306: MatGetLocalSize(A,&m,NULL); 307: PetscMalloc2((!!dnnz)*m,&sdnnz,(!!onnz)*m,&sonnz); 308: for (i=0; i<m; i++) { 309: if (dnnz) sdnnz[i] = dnnz[i/bs] * bs; 310: if (onnz) sonnz[i] = onnz[i/bs] * bs; 311: } 312: MatSeqAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL); 313: MatMPIAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL,0,onnz ? sonnz : NULL); [...] Though might something be happening later that reduces the amount of nonzeros allocated, since the "dense" blocks of the matrix actually will have zero entries that never get a value set? Something does appear to be screwy when I look at the "-snes_view" output for a time-dependent problem where I see these errors. When using BAIJ, at every time step I see Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes type: seqbaij rows=144, cols=144, bs=3 total: nonzeros=2304, allocated nonzeros=2304 total number of mallocs used during MatSetValues calls =0 block size is 3 but when I switch to AIJ, I initially see Mat Object: Mat_0x84000000_0 (flow_) 1 MPI processes type: seqaij rows=144, cols=144, bs=3 total: nonzeros=1584, allocated nonzeros=3324 total number of mallocs used during MatSetValues calls =68 using I-node routines: found 96 nodes, limit used is 5 but as things progress, the allocated nonzeros and mallocs count keeps growing; by step 43 I'm seeing total: nonzeros=1584, allocated nonzeros=115524 total number of mallocs used during MatSetValues calls =7548 If I dump the matrices and look at them in something like Octave, the matrices from the BAIJ and AIJ runs appear identical within round-off error, and we certainly aren't adding any entries at each step. Why should PETSc keep calling malloc() at each MatSetValues() call, then? I suspect a bug somewhere in the AIJ case call sequence of MatSetValuesBlockedLocal() --> MatSetValuesBlocked() --> MatSetValues() --> MatSetValues_SeqAIJ(). I have trouble following all of the logic in matsetvaluesseqaij_(), though, so I guess I'm going to have try harder to understand why MatSeqXAIJReallocateAIJ() is being hit there. Any educated guesses about what might be going wrong would be appreciated. There is a lot of PETSc code I'm not familiar with involved here. Cheers, Richard Barry (Clearly it *is* possible, but should it be?) I'm still trying to figure out if there is something wrong with what PFLOTRAN is doing, vs. something going wrong somewhere inside PETSc. Any hints about what to look at from someone with more familiarity with this code would be appreciated. --Richard

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Re: [petsc-dev] Errors in MatSetValuesBlockedLocal() when using AIJ, but not BAIJ!
by Smith, Barry F. 21 Feb '19

21 Feb '19

> On Feb 20, 2019, at 12:50 PM, Mills, Richard Tran via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > Folks, > > I'm working with some PFLOTRAN examples, and I've been scratching my head for a while at errors that are being generated in MatSetValuesBlockedLocal(), related to new nonzeros requiring a malloc. E.g., > > [0]PETSC ERROR: Argument out of range > [0]PETSC ERROR: New nonzero at (2,0) caused a malloc > > The strange thing is that all of these examples run fine when I use the PFLOTRAN default BAIJ matrix type (with blocks column-oriented) -- I only see the issue when I switch to using AIJ. If I set the matrix option MAT_NEW_NONZERO_ALLOCATION_ERR to PETSC_FALSE to allow things to run with AIJ, everything seems to work perfectly. (And once the Jacobian matrix is constructed the first time, the memory usage is not growing according to what I see from -malloc_log.) > > I've spent some time poking around with a debugger in the variants of MatSetValues() and MatXAIJSetPreallocation(), and I haven't been able make much progress in determining why I'm seeing this in AIJ vs. BAIJ -- it's easy to get confused looking at this code, and it's going to take me more time to follow what is going on than I've had to spare so far. So, I've got a few questions. First, should it even be possible to see what I am seeing? That is, if the MatSetValuesBlocked() routine is not causing new allocations when using BAIJ, should this be possible with AIJ? Sure, because the preallocation for BAIJ matrix is by block, while for AIJ it is by point (even if you provide a block size to AIJ). So long as the new entry is within an allocated block it will not trigger an error with BAIJ but may with AIJ. Barry > (Clearly it *is* possible, but should it be?) I'm still trying to figure out if there is something wrong with what PFLOTRAN is doing, vs. something going wrong somewhere inside PETSc. > > Any hints about what to look at from someone with more familiarity with this code would be appreciated. > > --Richard

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Re: [petsc-dev] DMKSP and pcfieldsplit
by Lawrence Mitchell 21 Feb '19

21 Feb '19

Hi Matt, all, > On 21 Feb 2019, at 18:17, Matthew Knepley <knepley(a)gmail.com> wrote: > > Here is why I did this. I wanted this to work > > https://bitbucket.org/petsc/petsc/src/4dbc1805575afffed4e440f1353fcfccbc893… > > The DMKSP is initialized by SNES to have a function which says "get your matrix from SNES". Without this, the subproblem could > not make the matrix. Now I changed the description of exactly what matrix it is making and stored that in the subDM. > > What is the right way to think about fixing this? I think that if the DM can create a field decomposition, it should also be able to transfer user callbacks from the parent to the subdms. > > That way, the DM (IOW me) can control how that happens. > > Yes, that is what I thought I was doing above. Preserving the callbacks that had been set in the original DM. > Maybe clarify what you think should happen. > > Or do I have the way this is supposed to work all wrong. Is the ComputeOperators callback I set meant to be completely agnostic, and it should get all the problem-specific information from the DM? > > I am doing this, but it does not have to be the only way things work. What I do not understand is how this change breaks your stuff. > If you were setting the DMKSP compute callback, it should just override what I am doing above. If not, why does me setting it here > screw it up? I've done some more digging, and the setup that breaks is: SNES with pcfieldsplit inside and rediscretised multigrid inside the fieldsplit. What is going on is, I think, the following: SNESSolve sets up a ComputeOperators on the KSP: KSP ksp; ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr); ierr = KSPSetComputeOperators(ksp,KSPComputeOperators_SNES,snes);CHKERRQ(ierr); ierr = DMCoarsenHookAdd(snes->dm,DMCoarsenHook_SNESVecSol,DMRestrictHook_SNESVecSol,snes);CHKERRQ(ierr); How does this callback know where to linearise around? Well, KSPComputeOperators_SNES does this: if (dmsave == snes->dm) X = snes->vec_sol; /* We are on the finest level */ else { /* We are on a coarser level, this vec was initialized using a DM restrict hook */ ierr = DMGetNamedGlobalVector(snes->dm,"SNESVecSol",&Xnamed);CHKERRQ(ierr); And the DMCoarsenHookAdd and DMRestrictHook_SNESVecSol ensure that /if we coarsen the DM associated with the SNES/ that state vector is transferred to the coarser levels. However, when we do PCFieldsplit and DMCreateFieldDecomposition, this restriction hook and connection to the state vector is gone. As a result, when I rediscretise on the coarse grids, I'm always linearising around a zero state. So I suppose that what should happen is that somewhere in fieldsplit, we need to transfer SNES state over and setup the appropriate restrict hooks. Cheers, Lawrence

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